CTCF Binding Polarity Determines Chromatin Looping

Mol Cell. 2015 Nov 19;60(4):676-84. doi: 10.1016/j.molcel.2015.09.023. Epub 2015 Oct 29.


CCCTC-binding factor (CTCF) is an architectural protein involved in the three-dimensional (3D) organization of chromatin. In this study, we assayed the 3D genomic contact profiles of a large number of CTCF binding sites with high-resolution 4C-seq. As recently reported, our data also suggest that chromatin loops preferentially form between CTCF binding sites oriented in a convergent manner. To directly test this, we used CRISPR/Cas9 genome editing to delete core CTCF binding sites in three loci, including the CTCF site in the Sox2 super-enhancer. In all instances, CTCF and cohesin recruitment were lost, and chromatin loops with distal, convergent CTCF sites were disrupted or destabilized. Re-insertion of oppositely oriented CTCF recognition sequences restored CTCF and cohesin recruitment, but did not re-establish chromatin loops. We conclude that CTCF binding polarity plays a functional role in the formation of higher-order chromatin structure.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Binding Sites
  • CCCTC-Binding Factor
  • CRISPR-Cas Systems
  • Cell Cycle Proteins / metabolism
  • Cell Line
  • Chromatin / chemistry*
  • Chromosomal Proteins, Non-Histone / metabolism
  • Embryonic Stem Cells / cytology
  • Mice
  • Protein Binding
  • Repressor Proteins / chemistry*
  • Repressor Proteins / metabolism*


  • CCCTC-Binding Factor
  • Cell Cycle Proteins
  • Chromatin
  • Chromosomal Proteins, Non-Histone
  • Ctcf protein, mouse
  • Repressor Proteins
  • cohesins

Associated data

  • GEO/GSE72720